process {
    withName: GATK4_CALCULATECONTAMINATION {
        ext.args   = { "-tumor-segmentation ${meta.id}.segmentation.table" }
    }

    withName: GATK4_FILTERMUTECTCALLS {
        ext.prefix = { "${meta.id}_filtered" }
    }

    withName: GATK4_GETPILEUPSUMMARIES_NORMAL {
        ext.prefix = { "${meta.id}.normal" }
    }

    withName: GATK4_GETPILEUPSUMMARIES_TUMOR {
        ext.prefix = { "${meta.id}.tumor" }
    }

    withName: GATK4_LEARNREADORIENTATIONMODEL {
        ext.prefix = { "${meta.id}.artifactprior" }
    }

    withName: GATK4_MUTECT2 {
        ext.args   = { "--f1r2-tar-gz ${meta.id}.f1r2.tar.gz --normal-sample normal" }
    }
}
